/*
 * Copyright (c) 2013 Genome Research Ltd.
 * Author(s): James Bonfield
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *    1. Redistributions of source code must retain the above copyright notice,
 *       this list of conditions and the following disclaimer.
 * 
 *    2. Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials provided
 *       with the distribution.
 * 
 *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
 *    Institute nor the names of its contributors may be used to endorse
 *    or promote products derived from this software without specific
 *    prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
 * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
 * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

/*! \file
 * Include cram.h instead.
 *
 * This is an internal part of the CRAM system and is automatically included
 * when you #include cram.h.
 *
 * Implements the decoding portion of CRAM I/O. Also see
 * cram_codecs.[ch] for the actual encoding functions themselves.
 */

#ifndef _CRAM_READ_H_
#define _CRAM_READ_H_

#ifdef __cplusplus
extern "C" {
#endif

/* ----------------------------------------------------------------------
 * CRAM sequence iterators.
 */

/*! Read the next cram record and return it as a cram_record.
 *
 * Note that to decode cram_record the caller will need to look up some data
 * in the current slice, pointed to by fd->ctr->slice. This is valid until
 * the next call to cram_get_seq (which may invalidate it).
 *
 * @return
 * Returns record pointer on success (do not free);
 *        NULL on failure
 */
cram_record *cram_get_seq(cram_fd *fd);

/*! Read the next cram record and convert it to a bam_seq_t struct.
 *
 * @return
 * Returns 0 on success;
 *        -1 on EOF or failure (check fd->err)
 */
int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);


/* ----------------------------------------------------------------------
 * Internal functions
 */

/*! INTERNAL:
 * Decodes a CRAM block compression header.
 *
 * @return
 * Returns header ptr on success;
 *         NULL on failure
 */
cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
							   cram_block *b);

/*! INTERNAL:
 * Decodes a CRAM (un)mapped slice header block.
 *
 * @return
 * Returns slice header ptr on success;
 *         NULL on failure
 */
cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);


/*! INTERNAL:
 * Decode an entire slice from container blocks. Fills out s->crecs[] array.
 *
 * @return
 * Returns 0 on success;
 *        -1 on failure
 */
int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
		      SAM_hdr *hdr);


#ifdef __cplusplus
}
#endif

#endif